Submission information
Submission Number: 16
Submission ID: 33
Submission UUID: 66512bae-68f5-4db4-8a7e-9842f335b916
Submission URI: /form/project
Created: Tue, 09/03/2019 - 13:20
Completed: Tue, 09/03/2019 - 13:20
Changed: Thu, 05/05/2022 - 04:50
Remote IP address: 130.215.55.243
Submitted by: John Griffin
Language: English
Is draft: No
Webform: Project
| Project Title | Facilitating Fusarium Oxysporum Computational Research |
|---|---|
| Program | Northeast |
| Project Leader | John Griffin |
| jgriffin@umass.edu | |
| Mobile Phone | |
| Work Phone | 413-545-9939 |
| Mentor(s) | John Griffin |
| Student-facilitator(s) | Brandon Cross |
| Mentee(s) | |
| Project Description | Li-Jun Ma at UMass Amherst uses high-throughput sequencing that relies on HPC. We have been adapting her PacBIO SMRTAnalysis pipelines to run in a cluster environment. We are working extensively with PacBIO vendor support, and with the Ask.CI and XSEDE Campus Champions communities to tackle this project. Ask.CI has proved very useful and allowed us to progress farther with one of the pieces of software for Li-jun. --- Li-Jun Ma, Associate Professor of Biology at UMass Amherst, is researching Fusarium oxysporum. This fungus causes wilt in over 100 plant species including tomato, cotton, watermelon and banana, costing farmers billions of dollars in losses worldwide each year. The disease is difficult to control. Once the soil is infected, the fungus can remain viable for 30 or 40 years, and at present there really is no way to control it. By advancing understanding of the molecular mechanism of fungal pathogenesis, she hopes to increase ways to develop disease-resistant crops. Dr. Ma uses high-throughput sequencing that relies on HPC. We have been adapting her PacBIO SMRTAnalysis pipelines to run in a cluster environment. We are working extensively with PacBIO vendor support, and with the Ask.CI and XSEDE Campus Champions communities to tackle this project. Ask.CI has proved very useful and allowed us to progress farther with one of the pieces of software for Li-jun. This work is supported by an NSF CAREER grant. Ma is also supported by a Burroughs Wellcome Fund award to understand pathogenesis and develop new treatment options for human infections caused by fungal pathogens in the same species. |
| Project Deliverables | * Functioning SMRT analysis pipeline on C3DDB cluster |
| Project Deliverables | |
| Student Research Computing Facilitator Profile | We have a student facilitator, Brandon Cross, who is a computer systems engineering student. He had no biology domain experience prior to this project. |
| Mentee Research Computing Profile | |
| Student Facilitator Programming Skill Level | |
| Mentee Programming Skill Level | |
| Project Institution | UMass Amherst / MGHPCC |
| Project Address | |
| Anchor Institution | NE-MGHPCC |
| Preferred Start Date | 09/25/2018 |
| Start as soon as possible. | No |
| Project Urgency | Already behind3Start date is flexible |
| Expected Project Duration (in months) | |
| Launch Presentation | |
| Launch Presentation Date | |
| Wrap Presentation | |
| Wrap Presentation Date | |
| Project Milestones | |
| Github Contributions | |
| Planned Portal Contributions (if any) | |
| Planned Publications (if any) | |
| What will the student learn? | Student has already learned: how to interface with a researcher outside their domain; how to adapt a program to run in a batch scheduled environment that was not designed for this environment; how to interface with vendor support and community support to tackle a complex problem; skills to deal with problems that remain unresolved. |
| What will the mentee learn? | |
| What will the Cyberteam program learn from this project? | This project is a test case for sustainability of the cyberteam initiative methods. The researcher reached out for help from MGHPCC. The Cyberteam initiative found the mentor, and the mentor found and funded the student. |
| HPC resources needed to complete this project? | Access to C3DDB |
| Notes | |
| What is the impact on the development of the principal discipline(s) of the project? | |
| What is the impact on other disciplines? | |
| Is there an impact physical resources that form infrastructure? | |
| Is there an impact on the development of human resources for research computing? | |
| Is there an impact on institutional resources that form infrastructure? | |
| Is there an impact on information resources that form infrastructure? | |
| Is there an impact on technology transfer? | |
| Is there an impact on society beyond science and technology? | |
| Lessons Learned | |
| Overall results |